HIV-1 dis kissing-loop in complex with lividomycin

Structure

x-ray diffraction · 1 distinct chain.

Ligands and binding sites

• LIV · (2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3, 5-diamino-2-((2S,3R,5S,6R)-3-amino-5-hydroxy-6-(hydroxymethyl)-tetrahydro-2H-pyran-2-yloxy)-6-hydroxycyclohexyloxy)-4-hydroxy-2-(hydroxymethyl)-tetrahydrofuran-3-yloxy)-4-hydroxy-tetrahydro-2H-pyran-3-yloxy)-6-(hydroxymethyl)-tetrahydro-2H-pyran-3,4,5-triol · ligand · 2 copies · chains A, B
• K · Potassium ion · metal · 4 copies · chains A, B
• CL · Chloride ion · ion · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 372 Ų buried · 29 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

• 2FD0 · HIV-1 DIS kissing-loop in complex with lividomycin · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Elsewhere: RCSB PDB 2FD0 · PDBe 2FD0